1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
|
// Copyright 2017 Global Phasing Ltd.
#include <cstdio> // for printf, fprintf
#include <cstdlib> // for atof
#include "gemmi/ccp4.hpp"
#include "gemmi/solmask.hpp" // for SolventMasker
#include "gemmi/symmetry.hpp"
#include "gemmi/mmread_gz.hpp" // for read_structure_gz
#include "timer.h"
#define GEMMI_PROG mask
#include "options.h"
namespace {
enum OptionIndex {
Timing=4, GridSpac, GridDims, Radius, RProbe, RShrink,
IslandLimit, Hydrogens, AnyOccupancy, CctbxCompat, RefmacCompat, Invert
};
struct MaskArg {
static option::ArgStatus FileFormat(const option::Option& option, bool msg) {
return Arg::Choice(option, msg, {"coor", "map", "none"});
}
};
const option::Descriptor Usage[] = {
{ NoOp, 0, "", "", Arg::None,
"Usage:\n " EXE_NAME " [options] INPUT output.msk"
"\n\nMakes a bulk-solvent mask in the CCP4 format."
"\nINPUT is a coordinate file (mmCIF, PDB, etc)." },
CommonUsage[Help],
CommonUsage[Version],
CommonUsage[Verbose],
{ Timing, 0, "", "timing", Arg::None,
" --timing \tPrint how long individual steps take." },
{ GridSpac, 0, "s", "spacing", Arg::Float,
" -s, --spacing=D \tMax. sampling for the grid (default: 1A)." },
{ GridDims, 0, "g", "grid", Arg::Int3,
" -g, --grid=NX,NY,NZ \tGrid sampling." },
{ Radius, 0, "r", "radius", Arg::Float,
" -r, --radius=R \tUse constant radius of atom spheres." },
{ RProbe, 0, "", "r-probe", Arg::Float,
" --r-probe=Rp \tUse VdW radius + Rp (default: 1.0A)." },
{ RShrink, 0, "", "r-shrink", Arg::Float,
" --r-shrink=Rs \tFinally, remove a shell of thickness Rs (default: 1.1A)." },
{ IslandLimit, 0, "", "island-limit", Arg::Float,
" --island-limit=VOL \tRemove \"islands\" up to VOL A^3." },
{ Hydrogens, 0, "", "hydrogens", Arg::None,
" --hydrogens \tDon't ignore hydrogens." },
{ AnyOccupancy, 0, "", "any-occupancy", Arg::None,
" --any-occupancy \tDon't ignore zero-occupancy atoms." },
{ CctbxCompat, 0, "", "cctbx-compat", Arg::None,
" --cctbx-compat \tUse vdW, Rprobe, Rshrink radii from cctbx." },
{ RefmacCompat, 0, "", "refmac-compat", Arg::None,
" --refmac-compat \tUse radii compatible with Refmac." },
{ Invert, 0, "I", "invert", Arg::None,
" -I, --invert \t0 for solvent, 1 for molecule." },
{ 0, 0, 0, 0, 0, 0 }
};
} // anonymous namespace
int GEMMI_MAIN(int argc, char **argv) {
OptParser p(EXE_NAME);
p.simple_parse(argc, argv, Usage);
p.require_positional_args(2);
const char* input = p.nonOption(0);
const char* output = p.nonOption(1);
p.check_exclusive_pair(GridDims, GridSpac);
p.check_exclusive_pair(CctbxCompat, RefmacCompat);
p.check_exclusive_pair(Radius, RProbe);
p.check_exclusive_pair(Radius, CctbxCompat);
p.check_exclusive_pair(Radius, RefmacCompat);
if (p.options[Verbose])
std::fprintf(stderr, "Converting %s ...\n", input);
try {
using std::int8_t;
Timer timer(p.options[Timing]);
gemmi::Structure st = gemmi::read_structure_gz(input);
gemmi::Ccp4<int8_t> mask;
mask.grid.unit_cell = st.cell;
mask.grid.spacegroup = st.find_spacegroup();
if (p.options[GridDims]) {
auto dims = parse_comma_separated_ints(p.options[GridDims].arg);
mask.grid.set_size(dims[0], dims[1], dims[2]);
} else {
double spac = 1;
if (p.options[GridSpac])
spac = std::atof(p.options[GridSpac].arg);
mask.grid.set_size_from_spacing(spac, gemmi::GridSizeRounding::Up);
}
if (p.options[Verbose]) {
const auto& g = mask.grid;
std::fprintf(stderr, "Grid: %d x %d x %d\n", g.nu, g.nv, g.nw);
std::fprintf(stderr, "Spacing: %.3f, %.3f, %.3f\n",
g.spacing[0], g.spacing[1], g.spacing[2]);
size_t np = g.data.size();
double vol = st.cell.volume;
std::fprintf(stderr, "Total points: %zu\n", np);
std::fprintf(stderr, "Unit cell volume: %.1f A^3\n", vol);
std::fprintf(stderr, "Volume per point: %.3f A^3\n", vol / np);
if (g.spacegroup) {
std::fprintf(stderr, "Spacegroup: %s\n", g.spacegroup->hm);
int na = g.spacegroup->operations().order();
std::fprintf(stderr, "ASU volume: %.1f A^3\n", vol / na);
std::fprintf(stderr, "Points per ASU: %.1f\n", double(np) / na);
} else {
std::fprintf(stderr, "No spacegroup\n");
}
}
if (st.models.size() > 1)
std::fprintf(stderr, "Note: only the first model is used.\n");
gemmi::SolventMasker masker(gemmi::AtomicRadiiSet::VanDerWaals);
if (p.options[Radius])
masker.set_radii(gemmi::AtomicRadiiSet::Constant,
std::atof(p.options[Radius].arg));
else if (p.options[CctbxCompat])
masker.set_radii(gemmi::AtomicRadiiSet::Cctbx);
else if (p.options[RefmacCompat])
masker.set_radii(gemmi::AtomicRadiiSet::Refmac);
if (p.options[RProbe])
masker.rprobe = std::atof(p.options[RProbe].arg);
if (p.options[RShrink])
masker.rshrink = std::atof(p.options[RShrink].arg);
if (p.options[Hydrogens])
masker.ignore_hydrogen = false;
if (p.options[AnyOccupancy])
masker.ignore_zero_occupancy_atoms = false;
timer.start();
masker.clear(mask.grid);
masker.mask_points(mask.grid, st.models[0]);
timer.print("Points masked in");
timer.start();
masker.symmetrize(mask.grid);
timer.print("Mask symmetrized in");
if (masker.rshrink > 0) {
timer.start();
masker.shrink(mask.grid);
timer.print("Mask shrunken in");
}
if (p.options[IslandLimit])
masker.island_min_volume = std::atof(p.options[IslandLimit].arg);
if (masker.island_min_volume > 0.) {
timer.start();
int n = masker.remove_islands(mask.grid);
timer.print("Islands removed in");
if (p.options[Verbose])
std::fprintf(stderr, "Islands removed: %d\n", n);
}
if (p.options[Verbose]) {
size_t n = std::count(mask.grid.data.begin(), mask.grid.data.end(), 0);
std::fprintf(stderr, "Points masked by model: %zu\n", n);
}
if (p.options[Invert])
masker.invert(mask.grid);
mask.update_ccp4_header(0);
mask.write_ccp4_map(output);
} catch (std::runtime_error& e) {
std::fprintf(stderr, "ERROR: %s\n", e.what());
return 1;
}
return 0;
}
|
